Method main_

src/topp/MapAlignerTreeGuided.cpp:157–234

  }

  ExitCodes main_(int, const char**) override
  {
    ExitCodes ret = checkParameters_();
    if (ret != EXECUTION_OK)
    {
      return ret;
    }
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------
    StringList in_files = getStringList_("in");
    StringList out_files = getStringList_("out");
    StringList out_trafos = getStringList_("trafo_out");
    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------
    Size in_files_size = in_files.size();
    FeatureXMLFile fxml_file;
    // define here because needed to load and store
    FeatureFileOptions param = fxml_file.getOptions();
    // to save memory don't load convex hulls and subordinates
    param.setLoadSubordinates(false);
    param.setLoadConvexHull(false);
    fxml_file.setOptions(param);

    vector<FeatureMap> feature_maps(in_files_size);
    loadInputMaps_(feature_maps, in_files, fxml_file);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    // constructing tree
    vector<vector<double>> maps_ranges(in_files_size);  // to save ranges for alignment (larger rt_range -> reference)
    std::vector<BinaryTreeNode> tree;    // to construct tree with pearson coefficient
    MapAlignmentAlgorithmTreeGuided algoTree;
    Param algo_params = getParam_().copy("algorithm:", true);
    algoTree.setParameters(algo_params);
    OpenMS::MapAlignmentAlgorithmTreeGuided::buildTree(feature_maps, tree, maps_ranges);

    // print tree
    ClusterAnalyzer ca;
    OPENMS_LOG_INFO << "  Alignment follows Newick tree: " << ca.newickTree(tree, true) << endl;

    // alignment
    vector<Size> trafo_order;
    FeatureMap map_transformed;
    // depending on the selected parameter, the input data for the alignment are copied or reloaded after alignment
    if (getStringOption_("copy_data") == "true")
    {
      vector<FeatureMap> copied_maps = feature_maps;
      algoTree.treeGuidedAlignment(tree, copied_maps, maps_ranges, map_transformed, trafo_order);
    }
    else
    {
      algoTree.treeGuidedAlignment(tree, feature_maps, maps_ranges, map_transformed, trafo_order);
      // load() of FeatureXMLFile clears featureMap, so we don't have to care
      loadInputMaps_(feature_maps, in_files, fxml_file);